EcDNA
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB50518 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8264078.fastq.gz | Fastqsanger.gz | |||
| ERR8264079.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA H3K27ac occupancy after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days and fixed for ChIPseq library preperation.
2026-07-02 | E-MTAB-16944 | biostudies-arrayexpress
Project description:Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.
2020-11-25 | GSE159972 | GEO
Project description:Extrachromosomal DNA (ecDNA) is a major driver of oncogene amplification, intratumoural heterogeneity and rapid genetic change. We observe that ecDNA frequently undergoes segregation errors and is incorporated into micronuclei (MN) in ecDNA positive cancer cells. Different ecDNA species can coalesce into MN and lead to asymmetric inheritance. EcDNA in MN undergoes epigenetic changes and shows decreased oncogene transcription. Cells harbouring ecDNA-positive MN show prolonged cell cycle progression and an increased likelihood of cell death. Here we assess ecDNA oncogene transcription after hydroxyurea treatment. COLO 320DM cells were treated with 80 µM hydroxyurea or DMSO (vehicle control) for 3 days. RNA was extracted and subjected to mRNA library preparation and single-end sequencing.
2026-07-02 | E-MTAB-16933 | biostudies-arrayexpress
Project description:Extrachromosomal DNA (ecDNA) is an important carrier for the amplification of proto-oncogenes. It can not only drive cancer progression by increasing the copy number of oncogenes but also influence the transcriptional regulation of oncogenes by increasing chromatin accessibility and regulating chromatin interactions. Currently, the generation of ecDNA is rather complex and the exact mechanism remains unclear. This study aims to investigate the molecular mechanism underlying the generation of ecDNA in order to identify the targets for ecDNA-targeted drug therapies. We analyzed the chromatin landscape in COLO320-DM and COLO320-HSR cells through CUT&Tag. The results of CUT&Tag for Lig3, the open chromatin marker H3K27ac, and the promoter marker H3K4me3 showed that Lig3 was specifically enriched in the MYC ecDNA amplification regions and bound to a large number of open chromatin regions and promoter regions, indicating that Lig3 may be related to the formation of ecDNA and stably bind to ecDNA, thereby maintaining the integrity of the genes carried by ecDNA. Furthermore, we found that there were a large number of merge peaks between Lig3 and YY1 across the whole genome, which were abundantly occupied at the MYC ecDNA amplification sites. Meanwhile, we observed that in COLO320-DM cells (where oncogenes are amplified in the form of ecDNA), there was a significant enrichment of YY1 in the MYC amplification regions, while in COLO320-HSR cells (where oncogenes are amplified on the homogeneously staining regions, HSR), the peaks of YY1 were significantly decreased. Our data suggest that YY1 is essential for the generation of ecDNA. It forms a complex with Lig3 to jointly regulate the formation of ecDNA, and this complex can be detected as it resides on ecDNA for a relatively long period of time. This may also be related to the stability of ecDNA and its involvement in genomic regulation.
2025-07-25 | GSE287200 | GEO
Project description:Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.
2021-05-24 | GSE175452 | GEO
Project description:Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.
2021-05-24 | GSE175451 | GEO
Project description:Extrachromosomal DNA (ecDNA) presents a major challenge for cancer patients. EcDNA renders tumours treatment-resistant by facilitating massive oncogene transcription and rapid genome evolution, contributing to poor patient survival. At present, there are no ecDNA-specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers. Stepwise analyses of ecDNA transcription reveal pervasive RNA transcription and associated single-stranded DNA (ssDNA), leading to excessive transcription replication conflicts and replication stress (RS) compared to chromosomal loci. Nucleotide incorporation on ecDNA is markedly slower, and RS is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. pRPA2-S33, a mediator of DNA damage repair that binds ssDNA, shows elevated localization on ecDNA in a transcription dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition abrogates the DNA replication check point, causing extensive and preferential tumour cell death in ecDNA-containing tumours. We advance a highly selective, potent, and bioavailable oral CHK1 inhibitor, BBI-2779, that preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 on ecDNA, BBI-2779 suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. Transcription replication conflict emerges as a target for ecDNA-directed therapy, exploiting a synthetic lethality of excess to treat cancer. This work was delivered as part of the eDyNAmiC team supported by the Cancer Grand Challenges partnership funded by Cancer Research UK (CGCATF-2021/100012 and CGCATF-2021/100025) and the National Cancer Institute (OT2CA278688 and OT2CA278635) to H.Y.C., P.S.M., and V.B. This project was supported by NIH RM1-HG007735 (H.Y.C., W.J.G., C.C.).
2024-05-23 | GSE249654 | GEO
Project description:In this study, we established ecDNA-containing cell models by either transfecting synthetic circular DNA or excising endogenous chromosomal DNA. We found that ecDNA can be stable maintained in these cell models. By identifying proteins on nascent DNA, we found DNA damage repair pathway was significantly enriched in ecDNA-containing cells. ecDNA can activate DNA damage response. Further evidence show that TOP2B and LIG3. The association of ecDNA replication with cell proliferation and DNA damage response was explored by comprehensive profiling and analysis. Utilizing EdU (5-ethynyl-2’-deoxyuridine)-immunoprecipitation-mass spectrometry (EdU-IP-MS), we identified critical regulators involved in ecDNA replication and examined their functional roles in cancer cell DNA damage response and proliferation.
2025-04-18 | PXD060725 | Pride
Project description:Single-cell DNA sequencing was performed using the Mission Bio Tapestri platform to analyze ecDNA-associated copy-number dynamics across cancer cell lines, single-cell-derived clones, and drug-treated conditions. Droplet-based targeted PCR amplification was carried out according to the manufacturer’s instructions using custom primer panels designed to quantify ecDNA-associated loci, control genomic regions, and barcode sequences. The dataset includes parental cancer cell lines, including COLO320DM, COLO320HSR, H2170, SNU-16, PC-3, and RPE1 control cells, as well as multiple COLO320DM-derived single-cell clones. Selected clones were analyzed under basal conditions and after drug treatment, including DMSO and JQ1. Sequencing libraries were prepared following the manufacturer’s protocol and sequenced using the Illumina NextSeq 550 platform with 2 × 75 bp paired-end reads.
2026-05-25 | E-MTAB-16119 | biostudies-arrayexpress
Project description:Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high oncogene expression through gene amplification and altered gene regulation. Gene induction typically involves cis regulatory elements that contact and activate genes on the same chromosome. Here we show that ecDNA hubs, clusters of ~10-100 ecDNAs within the nucleus, enable intermolecular enhancer-gene interactions to promote oncogene overexpression in trans. ecDNAs encoding multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumors. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the BET protein BRD4 in a MYC-amplified colorectal cancer cell line. BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-based oncogene transcription. A BRD4-bound promoter in PVT1 is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent MYC expression. PVT1 promoter on a heterologous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic CRISPRi silencing of ecDNA enhancers reveal intermolecular enhancer-gene activation among multiple oncogene loci amplified on distinct ecDNAs. Together, these results demonstrate that ecDNA hubs are protein-tethered clusters of ecDNAs which enable intermolecular transcriptional regulation. ecDNA hubs may act as units of oncogene function, cooperative evolution, and potential targets for cancer therapy.
2020-11-25 | GSE159985 | GEO